Structure of PDB 5jjs Chain A

Receptor sequence

>5jjsA (length=849) Species: 11069 (dengue virus type 3)

GETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAV
SRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTK
GGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPT
VEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLV
RNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDV
DLGAGTRHVNAEPETPNMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYH
GSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFK
EKVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTN
WDSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMSRAIWYMWLGVRYL
EFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADD
TAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPT
PTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADL
ENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALND
MGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDE
LIGRARISQGWSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPV
HWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWEN
VPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYMP

3D structure

• PDB: 5jjs Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling
• Chain: A
• Resolution: 1.65 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  3.4.21.91: flavivirin.
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	A	E437 H441 C446 C449	E420 H424 C429 C432
BS02	ZN	A	H712 H714 C728 C847	H679 H681 C695 C812
BS03	6L2	A	L511 C709 H711 R729 R737 M765 T794 W795 S796 H798 A799 H800 Q802 W803	L478 C676 H678 R696 R704 M730 T759 W760 S761 H763 A764 H765 Q767 W768	MOAD: ic50=0.048uM PDBbind-CN: -logKd/Ki=7.32,IC50=0.048uM
BS04	MG	A	D533 D664	D500 D631
BS05	SAH	A	S56 G58 G81 G86 W87 T104 K105 H110 E111 D131 V132 F133 D146	S51 G53 G76 G81 W82 T99 K100 H105 E106 D126 V127 F128 D141

Gene Ontology

Molecular Function

• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
• GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
• GO:0005524 ATP binding
• GO:0008168 methyltransferase activity

Biological Process

• GO:0032259 methylation
• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:5jjs, PDBe:5jjs, PDBj:5jjs
• PDBsum: 5jjs
• PubMed: 27500641
• UniProt: Q6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)